The HYDRA Uprising, also known as the HYDRA Infiltration and the Fall of S.H.I.E.L.D., was a major conflict that went back as early as the 1940s. After World War II, the security agency S.H.I.E.L.D. was founded, but was soon infiltrated by HYDRA, the rogue Nazi science group originally formed by the Red Skull prior to his disappearance.

For the next several decades, HYDRA grew within S.H.I.E.L.D.'s ranks, manipulating the agency and using its unlimited resources to suit their plans. In 2014, the infiltration was exposed during Project Insight, and HYDRA, in an effort to save itself, started purging all S.H.I.E.L.D. facilities of non-HYDRA aligned individuals.

After all of the undercover HYDRA agents had revealed themselves, the War on HYDRA began, letting the Avengers and the reformed S.H.I.E.L.D. fight HYDRA without being manipulated from the inside.

The group came into constant conflict with Captain America, who successfully disabled several of their facilities before confronting Schmidt at his headquarters. In the battle, Schmidt disappeared after physically handling the Tesseract, HYDRA was left without a leader and fell on the verge of collapse.[1]

Shortly after the end of the war, the peacekeeping agency S.H.I.E.L.D. was founded. Through Operation Paperclip, former HYDRA scientist Arnim Zola was recruited into S.H.I.E.L.D., but his recruitment proved to have dire consequences in the future. As a member of S.H.I.E.L.D., Zola sought out and provided access into the agency for several HYDRA operatives and loyalists that managed to escape justice after WWII. From within S.H.I.E.L.D., the new HYDRA grew like a parasite and slowly regained power.[2]

Secret War

"For 70 years HYDRA has been secretly feeding crises. Reaping war. And when history did not cooperate, history was changed. HYDRA created a world so chaotic that humanity is finally ready to sacrifice its freedom to gain its security. Once the purification process is complete, HYDRA's New World Order will arise."

Shortly after the war, Dr. Zola was able to find James Buchanan Barnes, Captain America's best friend, teammate and Zola's former test subject, who survived the fall from Zola's train in 1945, though he lost his left arm. Using S.H.I.E.L.D.'s resources, Zola continued his experiments on Barnes, brainwashing him and giving him the new cybernetic arm to replace his lost limb. Now blindly loyal to Zola and enhanced with another version of the Super Soldier Serum, Barnes became HYDRA's new fist, eventually gaining the nickname Winter Soldier.[2]

Over the next decades, HYDRA managed to rebuild much of its former strength. Secretly feeding crises around the globe, HYDRA created a world full of terrorist threats, wars, and dictators. And when some S.H.I.E.L.D. operatives would try to stop the terrorists, HYDRA would eliminate them, like one of S.H.I.E.L.D.'s founders Howard Stark and his wife Maria in 1991, though the world believed that they died in a car accident.[2][3]

The digitized consciousness of Arnim Zola, who resuscitated HYDRA from within S.H.I.E.L.D.

In 1972, Dr. Zola was diagnosed with a terminal illness. However, since he was one of the greatest scientific geniuses on the world, the leaders of S.H.I.E.L.D. decided to save his mind. Shortly before his physical death, Zola's consciousness was downloaded into a computer system located deeply beneath Camp Lehigh, S.H.I.E.L.D.'s first base. Continuing his existence as an artificially intelligent user interface, Zola created the 'Zola-algorithm' which was used by HYDRA to identify and target potential threats to its interests. Eventually, almost half of S.H.I.E.L.D. was composed of HYDRA's undercover agents or those who were corrupted and swore allegiance to HYDRA.

Troubles in Washington

After the battle of New York, the World Security Council granted S.H.I.E.L.D. more funds to invest in homeland security, for which "Project Insight" was created, a security network formed by three heavily-armed Helicarriers to protect the Earth. However, the leaders of HYDRA planned to use the Helicarriers to eliminate anyone who had been distinguished as a threat by Zola's algorithm.

As Nick Fury discovered that something dubious was going on, he secretly hired the French mercenary Georges Batroc and his gang of pirates to hijack the Lemurian Star, a S.H.I.E.L.D. ship related to Project Insight. During the rescue mission, the Black Widow would then have a chance to secretly recover confidential files.

After recovering the data, Fury attempted to open the files but discovered they were highly protected. He persuaded Pierce, his friend, to delay Project Insight as S.H.I.E.L.D. could have been compromised, not knowing that Pierce was in fact HYDRA's top undercover agent in S.H.I.E.L.D.[2]

A few hours after Fury's conversation with Pierce, a group of HYDRA agents disguised as cops attempted to kill Fury, but when he escaped them, the Winter Soldier intervened. Fury again managed to escape, though he was heavily wounded, and went to the apartment of the recently revived Steve Rogers, Captain America. When Rogers came home, Fury told him that S.H.I.E.L.D. had been compromised, when the Winter Soldier, who had followed Fury to the apartment, shot him from behind. Before falling unconscious, Fury gave Rogers the flash drive containing the files Black Widow had recovered.

Later, at the hospital, Fury apparently dies as his heart stops. However, that was only a ruse orchestrated by Fury himself. Agent Maria Hill asked to take care of the body and took him to a secret location for Doctor Fine to take care of his wounds. When Agent Brock Rumlow of the STRIKE team, actually an undercover HYDRA operative and Pierce's right hand man, came to the hospital to take Rogers to Pierce, Rogers hid Fury's USB in a vendor machine.

When Rogers arrived at the Triskelion, Pierce questioned him about the circumstances of Fury's death. Though Pierce told him that he and Fury were old friends, Rogers decided not to trust him and left his office. Pierce then gave the order to Rumlow and his men to capture Rogers.[2]

The Manhunt Begins

Steve Rogers escapes from the Triskelion.

"Captain Rogers has information regarding the death of Director Fury. Refused to share it. As difficult as this is to accept, Captain America is a fugitive from S.H.I.E.L.D."

As Rogers came into the elevator, Rumlow and a dozen other STRIKE team members joined him there. However, Rogers noticed that something was wrong, and they attacked him. When he defeated them, another team of heavily armed S.H.I.E.L.D. agents attempted to stop him, but he escaped by jumping out the elevator to avoid arrest. After surviving the fall he drove away on a motorcycle, though agent Jasper Sitwell, another HYDRA mole, set up a roadblock and sent a Quinjet to stop him. When Rogers escaped, Pierce told the S.H.I.E.L.D. agents at the Triskelion that Rogers is refusing to share information about Fury's death, and that he has become a fugitive. Later that night, the Winter Soldier came to Pierce's apartment, and he gave him orders to kill Rogers.[2]

Hunt for the Clairvoyant

Meanwhile, the team of Agent Phil Coulson was actively hunting the mysterious Clairvoyant, the man behind the Centipede Project, a scientific research and development group bent on recreating the Super Soldier. As their former colleague Mike Peterson, now transformed into the deadly cyborg Deathlok, attacked some of their colleagues, they tracked him to Pensacola, Florida, where he managed to escape, but they discovered Thomas Nash, a vegetative man on life support who introduced himself as Clairvoyant. He was immediately shot by Agent Grant Ward, a HYDRA mole, who did that on the order of the real Clairvoyant, John Garrett.[12]

Later, on their plane, the Bus, Leo Fitz discovered a secure line used by Melinda May. Believing her to be a traitor, Coulson and Skye accused her of treachery, not knowing that she was actually talking with Director Nick Fury. Suddenly, the S.H.I.E.L.D. technicians at the Hub, on the orders of Victoria Hand, hijacked the control of the Bus and rerouted it for the Hub. Hand believed that Coulson and his men work for the Clairvoyant and ordered her agents to eliminate them all when the plane touches the ground.[12] She also sent a pair of S.H.I.E.L.D. drones to attack and destroy John Garrett's plane.[13]

Back at the hospital, Rogers was reunited with his fellow colleague Natasha Romanoff, who retrieved Fury's USB some time earlier. When they went to an Apple store and tried to use one of the computers to see if there was any valuable information on the flash drive, Romanoff was unable to open the files. However, she managed to find the location where the USB could be unlocked, somewhere in New Jersey.

After evading the STRIKE team that was chasing them, Cap and Widow arrived at Camp Lehigh, an abandoned Army base where he was trained during World War II. Beneath the camp they discovered the old S.H.I.E.L.D. outpost housing dozens of old computers, but fitted with a modern USB interface. The computers came to life, revealing the digitized consciousness of Arnim Zola, who revealed them HYDRA's plan for world domination. While Zola was talking, HYDRA's operatives in S.H.I.E.L.D. launched two missiles at the base, blowing it up. However, Cap and Widow managed to survive the explosion and found refuge at the apartment of Sam Wilson.[2]

"S.H.I.E.L.D. is not what we thought it was. It's been taken over by HYDRA. Alexander Pierce is their leader. STRIKE and Insight crews are HYDRA as well. We don't know how many more, but I know they're in the building, they could be standing right next to you. They almost have what they want: absolute control."

Recruiting Captain America, Black Widow, Falcon, and Maria Hill to his cause, Fury created a way to destroy the Insight Helicarriers. While Hill, Captain America, and Falcon dealt with the Helicarriers, he and Black Widow dealt with Pierce. As the Helicarriers fell, one of them veered into the Triskelion, severely damaging the building. During the battle, many members of the World Security Council were killed and a message was sent out, revealing the truth about the HYDRA infiltration.[2]

"Phil, this is a battle for S.H.I.E.L.D.'s soul, and we're on the front lines. History will remember us this day.""That's right. It's for S.H.I.E.L.D.'s soul, and murder without consideration isn't..."

The same day, after the highjacking of the Bus' controls, the plane was flying toward the Hub. After surviving the attack from two S.H.I.E.L.D. drones, John Garrett boarded the Bus. Garrett and Coulson's team infiltrated the Hub with the intention of destroying it, thinking Hand to be HYDRA; it was eventually revealed, however, that the Battle of the Hub was largely staged, as Hand and an handful of agents had realized something was afoot and were secretly working against HYDRA.[13]

Other Assaults

"Captain America has defeated the Helicarriers at the Triskelion. But his status is unknown.""And S.H.I.E.L.D. has fallen.""HYDRA factions have taken control of our east African headquarters and the Treehouse. And those are just the ones we know of.""It's gonna be a scramble, a power grab."

Exposed, HYDRA immediately began covering their tracks, beginning on purging entire S.H.I.E.L.D. facilities of non-HYDRA agents and loyalists. While they successfully took over the Treehouse and the S.H.I.E.L.D. East African Headquarters, their attempted takeover of the Hub was thwarted by Phil Coulson and his team, aided by the revelation of Victoria Hand's true loyalties. Coulson's efforts led to the capture of HYDRA operative John Garrett, who managed to escape when Grant Ward murdered Agent Hand.[13] S.H.I.E.L.D. loyalists managed to defeat HYDRA's operatives at the Cube, forcing them to retreat.[14] A fierce battle was fought for the control of the aircraft carrier Iliad, but HYDRA's moles were ultimately defeated.[15] HYDRA brainwashedDonnie Gill and used him as a one-man army in order to take the Sandbox.[16]

New Battles

Outlawed

In light of the new information, the U.S. government questioned the organization's existence in several hearings. As a direct result of the events, Captain America and the Black Widow both left S.H.I.E.L.D., along with many other agents.[2] Eventually, because of how deep HYDRA's infiltration in S.H.I.E.L.D. was, the agency was internationally labeled a terrorist organization.[13][14]

Ward went to Providence thinking that he convinced Skye that the others needed her to decrypt the hard drive; he did not know that she knew he was a double-agent after she discovered the body of Eric Koenig. Skye went with Ward because she cared about him and wanted to know how he could betray them.[18]

Skye lied, telling Ward that the hard drive was location-based, taking him to Ruthie's Skillet, where she tried to escape. Deathlok, Ward's back-up, caught her and, after inducing a heart attack in Ward, got Skye to decrypt the drive. Finally, Phil Coulson, with Maria Hill as a distraction, saved Skye by dropping out the Bus in Lola.[19]

"It'll be just the four of us. We'll be outmanned and outgunned. But Fury always said... a man can accomplish anything when he realizes he's a part of something bigger. A team of people who share that conviction can change the world. So, what do you say? You ready to change the world?""No. But I'm ready to kick some ass."

Many agents in the United States went into hiding to avoid persecution, such as Kara Palamas.[22] Though Coulson attempted to find her, HYDRA got to her first, causing Coulson to believe that the two organizations were recruiting from the same pool of candidates.[23] He was more successful with others such as Noelle Walters and her team, stationed in the Netherlands.[24]

Disillusioned Agents

"When I got out of the hospital it turned out there had never been a S.H.I.E.L.D., just HYDRA hiding behind one. I signed up to protect the world from these dangerous alien elements.""We still do that.""The hell you do, you use them, unleash them, you've got those freaks working for you. Hell Phil, you are one. Makes me sick."

Despite Phil Coulson's efforts to rebuild S.H.I.E.L.D. and continue their goals, not all agents could look past HYDRA's deception. Felix Blake was disgusted by what the HYDRA Uprising had done so he refused to return to S.H.I.E.L.D. and instead created the Watchdogs, a team of radicals dedicated to hunting down and killing any and all Inhumans. Blake made a deal with Giyera to gain more weapons, unaware that Giyera was working for HYDRA's ancient Inhuman leader Hive.[25]